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- PDB-4a5r: Crystal structure of class A beta-lactamase from Bacillus licheni... -

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Basic information

Entry
Database: PDB / ID: 4a5r
TitleCrystal structure of class A beta-lactamase from Bacillus licheniformis BS3 with tazobactam
ComponentsBETA-LACTAMASE
KeywordsHYDROLASE
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / CARBON DIOXIDE / TRIETHYLENE GLYCOL / TAZOBACTAM INTERMEDIATE / Beta-lactamase
Similarity search - Component
Biological speciesBACILLUS LICHENIFORMIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPower, P. / Sauvage, E. / Herman, R. / Kerff, F. / Charlier, P.
CitationJournal: To be Published
Title: Crystal Structure of Class a Beta-Lactamase from Bacillus Licheniformis Inhibited by Tazobactam
Authors: Power, P. / Herman, R. / Kerff, F. / Mercuri, P. / Galleni, M. / Gutkind, G. / Charlier, P. / Sauvage, E.
History
DepositionOct 28, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BETA-LACTAMASE
B: BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0628
Polymers59,0272
Non-polymers1,0356
Water5,080282
1
A: BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1584
Polymers29,5131
Non-polymers6453
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9044
Polymers29,5131
Non-polymers3903
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.955, 103.550, 63.732
Angle α, β, γ (deg.)90.00, 94.77, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein BETA-LACTAMASE / / CLASS A BETA-LACTAMASE


Mass: 29513.303 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) BACILLUS LICHENIFORMIS (bacteria) / Strain: BS3 / References: UniProt: P94458, beta-lactamase

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Non-polymers , 5 types, 288 molecules

#2: Chemical ChemComp-TBE / TAZOBACTAM INTERMEDIATE


Mass: 302.307 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N4O5S
#3: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-CO2 / CARBON DIOXIDE / Carbon dioxide


Mass: 44.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 282 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 50.8 % / Description: NONE
Crystal growpH: 4 / Details: pH 4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9686
DetectorType: MARRESEARCH SX-165 / Detector: CCD / Date: Sep 29, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.1→36.26 Å / Num. obs: 35366 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.7
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.5 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Y91

2y91


Resolution: 2.1→34.72 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.924 / Cross valid method: THROUGHOUT / ESU R: 0.204 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.23344 1764 5 %RANDOM
Rwork0.18208 ---
obs0.18469 33545 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.244 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å2-0.01 Å2
2--0.44 Å20 Å2
3----0.53 Å2
Refinement stepCycle: LAST / Resolution: 2.1→34.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4022 0 69 282 4373
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224149
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2361.9935607
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0615512
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.05625.213188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.37415748
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9551528
X-RAY DIFFRACTIONr_chiral_restr0.0890.2646
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213078
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1091.52564
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.79124134
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.25231585
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.9384.51473
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 127 -
Rwork0.267 2462 -
obs--99.58 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.5831-4.5952-1.84343.86640.50875.0554-0.1001-0.42790.14970.30130.038-0.341-0.22930.42470.06210.1087-0.0517-0.04480.2210.00670.248738.7374.1628.233
20.5885-0.2745-0.18150.9782-0.06190.9044-0.01330.0493-0.0090.02370.01130.1211-0.0122-0.00510.00210.20850.00440.0110.1583-0.0010.273715.0643.01223.031
35.1358-0.708-7.92274.7064.899415.5264-0.38580.5115-0.1212-0.5880.2403-0.1060.2607-0.52740.14550.55160.0106-0.03150.13440.01440.207415.38-7.7592.138
41.07750.21540.26641.35390.04811.5446-0.05140.111-0.0186-0.09720.05820.04120.0111-0.0229-0.00670.18670.00620.00790.16080.00330.254515.0052.51413.774
52.3502-0.2956-0.28540.9059-0.11271.5622-0.0107-0.1694-0.18150.17760.00090.06920.0761-0.05370.00980.20720.00920.00790.113-0.00660.270317.897-4.48527.788
62.83540.2663-0.97941.6285-0.55473.11320.0084-0.0052-0.07760.1443-0.0355-0.25570.04890.21660.02720.12820.0007-0.01120.1796-0.00710.278532.183-0.57926.009
70.798-0.16080.51130.92080.01941.7211-0.0670.09160.0583-0.0957-0.0211-0.2026-0.13780.10280.08810.2246-0.02820.00940.11890.01470.255520.92519.58548.109
811.98062.04713.36456.23473.463611.3072-0.38970.0971-0.67280.24850.1970.45490.168-2.12310.19280.0531-0.00830.08870.67060.00170.1509-6.08416.19662.546
92.4642-0.4508-0.26853.05010.03133.9743-0.081-0.2563-0.1574-0.01090.1910.12260.1804-0.8506-0.11010.0777-0.0683-0.01120.25440.0260.18772.6811.84958.287
101.2122-0.0261-0.24660.7564-0.77152.3608-0.0081-0.1831-0.08580.00960.0506-0.0989-0.0073-0-0.04250.221-0.01340.00970.1266-0.00070.248115.57512.18957.463
111.78870.3173-0.06611.7991-0.66262.5806-0.08510.14870.0336-0.23650.10110.183-0.107-0.5338-0.0160.19940.0227-0.03390.13940.00270.22077.19221.19745.009
123.08890.64990.71691.92160.10342.0406-0.0816-0.02080.2645-0.0031-0.0537-0.1726-0.24390.10360.13540.2562-0.0194-0.02750.09260.02280.316720.59127.38650.36
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A30 - 46
2X-RAY DIFFRACTION2A47 - 57
3X-RAY DIFFRACTION2A59 - 83
4X-RAY DIFFRACTION2A86 - 96
5X-RAY DIFFRACTION3A97 - 107
6X-RAY DIFFRACTION4A108 - 192
7X-RAY DIFFRACTION5A193 - 238
8X-RAY DIFFRACTION5A240 - 252
9X-RAY DIFFRACTION5A254 - 257
10X-RAY DIFFRACTION6A258 - 291
11X-RAY DIFFRACTION7B30 - 80
12X-RAY DIFFRACTION7B59 - 83
13X-RAY DIFFRACTION7B86 - 96
14X-RAY DIFFRACTION8B97 - 117
15X-RAY DIFFRACTION9B118 - 155
16X-RAY DIFFRACTION10B156 - 194
17X-RAY DIFFRACTION11B195 - 238
18X-RAY DIFFRACTION11B240 - 252
19X-RAY DIFFRACTION11B254 - 257
20X-RAY DIFFRACTION12B258 - 291

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